Amitay Isaacs solved the problem on the mailing list:
Some files in private/dns/sam.ldb.d/ have to hard links to files in private/sam.ldb.d/.
Maybe through a copy of the samba-folder or a restore in the past, the hardlinking got lost and the content of the two folders differ, because it were separate files then.
Amitay Isaacs solution that fixed it for me:
# cd dns/sam.ldb.d
# rm DC%3DDOMAINDNSZONES,DC%3DMUC,DC%3DMEDIZINISCHE-GENETIK,DC%3DDE.ldb
# rm DC%3DFORESTDNSZONES,DC%3DMUC,DC%3DMEDIZINISCHE-GENETIK,DC%3DDE.ldb
# rm metadata.tdb
# ln ../../sam.ldb.d/DC%3DDOMAINDNSZONES,DC%3DMUC,DC%3DMEDIZINISCHE-GENETIK,DC%3DDE.ldb .
# ln ../../sam.ldb.d/DC%3DFORESTDNSZONES,DC%3DMUC,DC%3DMEDIZINISCHE-GENETIK,DC%3DDE.ldb
# ln ../../sam.ldb.d/metadata.tdb .
Is there a special reason for hardlinking? Softlinks seem to be less dangerous when copying or moving (across filesystems)?
But one issue about adding DNS entries left:
If I add a new entry e. g. with samba-tool, I have to restart samba, before I can query the new record:
# samba-tool dns add 192.168.29.2 muc.medizinische-genetik.de marc9 A 192.168.29.70 -Uadministrator
Password for [MUC\administrator]:
Record added successfully
# host -t A marc9.muc.medizinische-genetik.de.
Host marc9.muc.medizinische-genetik.de. not found: 3(NXDOMAIN)
# /etc/init.d/rc.samba4 restart
Shutting down samba4: [ OK ]
Starting samba4: [ OK ]
# host -t A marc9.muc.medizinische-genetik.de.
marc9.muc.medizinische-genetik.de has address 192.168.29.70

I can't reproduce the issue any more (rc5 and rc6):
# samba-tool dns add 192.168.29.2 muc.medizinische-genetik.de marc9 A 192.168.29.70 -Uadministrator
Password for [MUC\administrator]:
Record added successfully
# host -t A marc9.muc.medizinische-genetik.de.
marc9.muc.medizinische-genetik.de has address 192.168.29.70
Works without restaring now. So this bug report can be closed.